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Topic:Genomics
Genomics in horses involves the study and analysis of the horse genome to understand genetic variations and their implications for equine health, performance, and breeding. This field encompasses the identification and mapping of genes associated with specific traits, diseases, and conditions in horses. Techniques such as whole-genome sequencing and genome-wide association studies (GWAS) are employed to explore genetic diversity and inheritance patterns among different horse breeds. Genomics provides insights into hereditary disorders, informs selective breeding practices, and aids in the development of personalized veterinary care. This page compiles peer-reviewed research studies and scholarly articles that explore the applications, methodologies, and findings of genomic research in equine science.
Harnessing the genetic toolbox for the benefit of the racing Thoroughbred. The understanding and application of genetics have grown extremely quickly since it has become possible to sequence the whole genome of an organism. The human genome sequence was completed in 2001 and that of the horse in 2007. The significance of this is that it makes it more feasible to explain how both genetically simple and complex traits are transmitted from one generation to the next and, therefore, to make informed breeding decisions, modify how horses are managed and trained to minimise the risk of disease and injury, and improve methods of prevention, diagnosis and treatment of many c...
A genome-wide association study of osteochondritis dissecans in the Thoroughbred. Osteochondrosis is a developmental orthopaedic disease that occurs in horses, other livestock species, companion animal species, and humans. The principal aim of this study was to identify quantitative trait loci (QTL) associated with osteochondritis dissecans (OCD) in the Thoroughbred using a genome-wide association study. A secondary objective was to test the effect of previously identified QTL in the current population. Over 300 horses, classified as cases or controls according to clinical findings, were genotyped for the Illumina Equine SNP50 BeadChip. An animal model was first implemented...
Genetic differences in the serum proteome of horses, donkeys and mules are detectable by protein profiling. Although horses and donkeys belong to the same genus, their genetic characteristics probably result in specific proteomes and post-translational modifications (PTM) of proteins. Since PTM can alter protein properties, specific PTM may contribute to species-specific characteristics. Therefore, the aim of the present study was to analyse differences in serum protein profiles of horses and donkeys as well as mules, which combine the genetic backgrounds of both species. Additionally, changes in PTM of the protein transthyretin (TTR) were analysed. Serum protein profiles of each species (five anima...
Genetic stability in the Icelandic horse breed. Despite the Icelandic horse enjoying great popularity worldwide, the breed's gene pool is small. This is because of a millennium of isolation on Iceland, population crashes caused by natural disasters and selective breeding. Populations with small effective population sizes are considered to be more at risk of selection pressures such as disease and environmental change. By analysing historic and modern mitochondrial DNA sequences and nuclear coat colour genes, we examined real-time population dynamics in the Icelandic horse over the last 150 years. Despite the small gene pool of this breed, w...
Equine fetal sex determination using circulating cell-free fetal DNA (ccffDNA). In this study, polymerase chain reaction (PCR) reamplification of the first PCR product (2nd-PCR) and a qPCR assay were used to detect the sex determining region Y (SRY) gene from circulating cell-free fetal DNA (ccffDNA) in blood plasma of pregnant mares to determine fetal sex. The ccffDNA was isolated from plasma of 20 Thoroughbred mares (5-13 y old) in the final 3 mo of pregnancy (fetal sex was verified after foaling). For controls, plasma from two non-pregnant mares and two virgin mares were used, in addition to the non-template control. The 182 bp nucleotide sequence corresponding to the ...
A genome-wide association study for quantitative trait loci of show-jumping in Hanoverian warmblood horses. Show-jumping is an economically important breeding goal in Hanoverian warmblood horses. The aim of this study was a genome-wide association study (GWAS) for quantitative trait loci (QTL) for show-jumping in Hanoverian warmblood horses, employing the Illumina equine SNP50 Beadchip. For our analyses, we genotyped 115 stallions of the National State stud of Lower Saxony. The show-jumping talent of a horse includes style and ability in free-jumping. To control spurious associations based on population stratification, two different mixed linear animal model (MLM) approaches were employed, besides l...
Genome-wide association study among four horse breeds identifies a common haplotype associated with in vitro CD3+ T cell susceptibility/resistance to equine arteritis virus infection. Previously, we have shown that horses could be divided into susceptible and resistant groups based on an in vitro assay using dual-color flow cytometric analysis of CD3+ T cells infected with equine arteritis virus (EAV). Here, we demonstrate that the differences in in vitro susceptibility of equine CD3+ T lymphocytes to EAV infection have a genetic basis. To investigate the possible hereditary basis for this trait, we conducted a genome-wide association study (GWAS) to compare susceptible and resistant phenotypes. Testing of 267 DNA samples from four horse breeds that had a susceptible or a r...
Genetic analysis of the Venezuelan Criollo horse. Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger ...
Genomic structure, polymorphism and expression of the horse alpha-actinin-3 gene. Gene characterization is an important feature for genome annotation and more particularly for candidate genes that could be selected in domestic species. Associations between an alpha-actinin-3 gene polymorphism and muscle performance were reported in humans involving a nonsense mutation (R577X) and in mice after inactivation of the gene. Here, we characterized the equine alpha-actinin-3 (ACTN3) gene by sequencing and transcript analysis. The cDNA was determined to be 3.47 kb in length with an open reading frame of 2709 bp expectedly encoding a protein 902 amino acids long. The ACTN3 gene is 1...
Transcriptome analysis of muscle in horses suffering from recurrent exertional rhabdomyolysis revealed energetic pathway alterations and disruption in the cytosolic calcium regulation. Recurrent exertional rhabdomyolysis (RER) is frequently observed in race horses like trotters. Some predisposing genetic factors have been described in epidemiological studies. However, the exact aetiology is still unknown. A calcium homeostasis disruption was suspected in previous experimental studies, and we suggested that a transcriptome analysis of RER muscles would be a possible way to investigate the pathway disorder. The purpose of this study was to compare the gene expression profile of RER vs. control muscles in the French Trotter to determine any metabolic or structural disruption. T...
The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip. We have used linkage disequilibrium (LD) to identify single nucleotide polymorphisms (SNPs) on the Illumina Equine SNP50 BeadChip, which may be incorrectly positioned on the genome map. A total of 1201 Thoroughbred horses were genotyped using the Illumina Equine SNP50 BeadChip. LD was evaluated in a pairwise fashion between all autosomal SNPs, both within and across chromosomes. Filters were then applied to the data, firstly to identify SNPs that may have been mapped to the wrong chromosome and secondly to identify SNPs that may have been incorrectly positioned within chromosomes. We identifie...
Thermophilic helicase-dependent DNA amplification using the IsoAmp™ SE experimental kit for rapid detection of Streptococcus equi subspecies equi in clinical samples. A simple and portable assay for detection of Streptococcus equi subspecies equi has been developed based on amplification of S. equi-specific sequence using a thermophilic helicase-dependent reaction followed by visual detection of the amplicon in a disposable lateral flow cassette. An experimental kit (IsoAmpâ„¢ SE) was evaluated. Analytical sensitivity was 50 copies of S. equi genomic DNA per reaction. The IsoAmp SE assay had 100% specificity when applied to nasal swabs and washes. The assay was more sensitive than culture but less sensitive than nested polymerase chain reaction (PCR). The t...
Discovery of lost diversity of paternal horse lineages using ancient DNA. Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA ...
Genetic characterization of equine adenovirus type 1. Two known serotypes of equine adenovirus (EAdV), equine adenovirus type 1 (EAdV-1) and equine adenovirus type 2 (EAdV-2) have been isolated from horses. EAdV-1 is predominantly associated with upper respiratory tract infections while EAdV-2 appears to be associated with gastrointestinal infections in horses. In this report the EAdV-1 genome has been sequenced for the first time. The EAdV-1 genome encoded genes are characteristic of the Mastadenovirus genus such as protein V and IX. Unexpectedly, phylogenetic reconstructions also revealed a close relationship between EAdV-1 and two recently cha...
Comparison of genomic and proteomic data in recurrent airway obstruction affected horses using Ingenuity Pathway Analysis®. Recurrent airway obstruction (RAO) is a severe chronic respiratory disease affecting horses worldwide, though mostly in the Northern hemisphere. Environmental as well as genetic factors strongly influence the course and prognosis of the disease. Research has been focused on characterization of immunologic factors contributing to inflammatory responses, on genetic linkage analysis, and, more recently, on proteomic analysis of airway secretions from affected horses. The goal of this study was to investigate the interactions between eight candidate genes previously identified in a genetic linkage...
Isolation and characterization of multipotent mesenchymal stromal cells from the gingiva and the periodontal ligament of the horse. The equine periodontium provides tooth support and lifelong tooth eruption on a remarkable scale. These functions require continuous tissue remodeling. It is assumed that multipotent mesenchymal stromal cells (MSC) reside in the periodontal ligament (PDL) and play a crucial role in regulating physiological periodontal tissue regeneration. The aim of this study was to isolate and characterize equine periodontal MSC. Tissue samples were obtained from four healthy horses. Primary cell populations were harvested and cultured from the gingiva, from three horizontal levels of the PDL (apical, midtoo...
True single-molecule DNA sequencing of a pleistocene horse bone. Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-...
A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski’s horses. The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitoch...
Chromosomal assignment of six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) in four species of the genus Equus. We mapped six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) on the chromosomes of Equus caballus, Equus asinus, Equus grevyi, and Equus burchelli by fluorescence in situ hybridization. Our results add six type I markers to the cytogenetic map of these species and provide new information on the comparative genomics of the genus Equus.
Streptococcus equi: a pathogen restricted to one host. Strangles caused by the host adapted Lancefield group C Streptococcus equi subspecies equi (S. equi) is a frequently diagnosed infectious disease of horses worldwide. Critical to the global success of S. equi is its ability to establish persistent infections within the guttural pouches of recovered apparently healthy horses that can result in transmission to in-contact animals. Recent research has identified key events in the S. equi genome, which occurred during its evolution from an ancestral strain of S. equi subspecies zooepidemicus, that may enhance its ability to evade host innate immune...
Identification of a mutation associated with fatal Foal Immunodeficiency Syndrome in the Fell and Dales pony. The Fell and Dales are rare native UK pony breeds at risk due to falling numbers, in-breeding, and inherited disease. Specifically, the lethal Mendelian recessive disease Foal Immunodeficiency Syndrome (FIS), which manifests as B-lymphocyte immunodeficiency and progressive anemia, is a substantial threat. A significant percentage (∼10%) of the Fell ponies born each year dies from FIS, compromising the long-term survival of this breed. Moreover, the likely spread of FIS into other breeds is of major concern. Indeed, FIS was identified in the Dales pony, a related breed, during the course of t...
Acinetobacter baumannii isolates from pets and horses in Switzerland: molecular characterization and clinical data. We investigated whether Acinetobacter baumannii isolates of veterinary origin shared common molecular characteristics with those described in humans. Methods: Nineteen A. baumannii isolates collected in pets and horses were analysed. Clonality was studied using repetitive extragenic palindromic PCR (rep-PCR) and multilocus sequence typing (MLST). PCR and DNA sequencing for various β-lactamase, aminoglycoside-modifying enzyme, gyrA and parC, ISAba1 and IS1133, adeR and adeS of the AdeABC efflux pump, carO porin and class 1/2/3 integron genes were performed. Results: Two main clones [A (n =â€...
Results of a haplotype-based GWAS for recurrent laryngeal neuropathy in the horse. Recurrent laryngeal neuropathy (RLN) is a major upper-airway disease of horses that causes abnormal respiratory noise during exercise and can impair performance. Etiopathogenesis remains unclear but genetic factors have been suspected for many decades. The objective of this study was to identify risk loci associated with RLN. To that end we genotyped 234 cases (196 Warmbloods, 20 Trotters, 14 Thoroughbreds, and 4 Draft horses), 228 breed-matched controls, and 69 parents with the Illumina Equine SNP50 BeadChip. Using these data, we quantified population structure and performed single-marker and...
Embryonic stem cells and iPS cells: sources and characteristics. The field of regenerative medicine research is rapidly expanding. One area of interest to equine researchers is the possibility of isolating or generating pluripotent cells, capable of producing differentiated cell types derived from all 3 primary germ layers. Reports of equine embryonic stem-like (ES) cell isolation can be found in the literature. Other groups are working to produce equine-induced pluripotent stem (iPS) cells. This article summarizes the essential features needed to characterize a cell type as pluripotent, specific challenges in using the horse as a model organism for pluripo...
Size-sieved subpopulations of mesenchymal stem cells from intervascular and perivascular equine umbilical cord matrix. Umbilical cord matrix (UCM) has been recently proposed as an alternative source of mesenchymal stem cells (MSCs). The aim of this study was to isolate and characterize presumptive stem cells from intervascular and perivascular equine UCM and to obtain homogeneous subpopulations from both sites. Methods: Umbilical cords were processed for retrieval of MSCs. Unsieved cells from intervascular and perivascular portions were evaluated for cell cycle analysis and for immunophenotyping by flow cytometry. Cells from each site were separated into larger and smaller sieved populations using multi-dishes...
Direct delayed human adenoviral BMP-2 or BMP-6 gene therapy for bone and cartilage regeneration in a pony osteochondral model. To evaluate healing of surgically created large osteochondral defects in a weight-bearing femoral condyle in response to delayed percutaneous direct injection of adenoviral (Ad) vectors containing coding regions for either human bone morphogenetic proteins 2 (BMP-2) or -6. Methods: Four 13mm diameter and 7mm depth circular osteochondral defects were drilled, 1/femoral condyle (n=20 defects in five ponies). At 2 weeks, Ad-BMP-2, Ad-BMP-6, Ad-green fluorescent protein (GFP), or saline was percutaneously injected into the central drill hole of the defect. Quantitative magnetic resonance imaging (...
Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus). Information on endogenous retroviruses fixed in the horse (Equus caballus) genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus), was 10434 nucleotide (nt) in length with the usual retroviral genome structure of 5'...
Reviewe: Genetics and genomics in equine exercise physiology: an overview of the new applications of molecular biology as positive and negative markers of performance and health. Equine breeding selection has been developed by applying quantitative genetic methods for calculating the heritability of the complex traits such as performance in racing or sport competitions. With the great development of biotechnologies, equine molecular genetics has come of age. The recent sequencing of the equine genome by an international consortium was a major advance that will impact equine genomics in the near future. With the rapid progress in equine genetics, new applications in early performance evaluation and the detection of disease markers become available. Many new biomolecular...
Association of sequence variants in CKM (creatine kinase, muscle) and COX4I2 (cytochrome c oxidase, subunit 4, isoform 2) genes with racing performance in Thoroughbred horses. The wild progenitors of the domestic horse were subject to natural selection for speed and stamina for millennia. Uniquely, this process has been augmented in Thoroughbreds, which have undergone at least 3 centuries of intense artificial selection for athletic phenotypes. While the phenotypic adaptations to exercise are well described, only a small number of the underlying genetic variants contributing to these phenotypes have been reported. Objective: A panel of candidate performance-related genes was examined for DNA sequence variation in Thoroughbreds and the association with racecourse per...
